4ZK4 | pdb_00004zk4

Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with 7-(5-isopropoxy-pyridin-3-yl)-1-methyl-1,7-diaza-spiro[4.4]nonane

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BYN	PDB entries 2BYN, 2BYP, 2BYR, 2BYS, 2PGZ, 3C79, 3C84
experimental model	PDB	2BYP	PDB entries 2BYN, 2BYP, 2BYR, 2BYS, 2PGZ, 3C79, 3C84
experimental model	PDB	2BYR	PDB entries 2BYN, 2BYP, 2BYR, 2BYS, 2PGZ, 3C79, 3C84
experimental model	PDB	2BYS	PDB entries 2BYN, 2BYP, 2BYR, 2BYS, 2PGZ, 3C79, 3C84
experimental model	PDB	2PGZ	PDB entries 2BYN, 2BYP, 2BYR, 2BYS, 2PGZ, 3C79, 3C84
experimental model	PDB	3C79	PDB entries 2BYN, 2BYP, 2BYR, 2BYS, 2PGZ, 3C79, 3C84
experimental model	PDB	3C84	PDB entries 2BYN, 2BYP, 2BYR, 2BYS, 2PGZ, 3C79, 3C84

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	1.7% PEG400, 0.085 M HEPES sodium, pH 7.5, 1.7 M ammonium sulfate, 15% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.662	α = 90
b = 78.205	β = 94.97
c = 120.465	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	88	CCD	ADSC QUANTUM 315r		2011-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.999	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.85	50	99.7	0.086	13.9	7.3		110948			25.09

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88	95.9		0.584		5	5294

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB entries 2BYN, 2BYP, 2BYR, 2BYS, 2PGZ, 3C79, 3C84	1.901	49.135	1.34	102638	5132	99.76	0.1826	0.1811	0.18	0.2125	0.21	32.2759

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.541
f_angle_d	1.318
f_chiral_restr	0.052
f_bond_d	0.014
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7974
Nucleic Acid Atoms
Solvent Atoms	439
Heterogen Atoms	148

Software

Software
Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.